IMHO only the boredom is a problem here. I mean, you can build the downtown and simply not use it yet. That might save you from having to design it later.
But the boredom, ah, that's an issue which needs to be addressed. It kills neighbourhoods more quickly than any plague!
Yes, the idea is that aliens are townies (although having extra human townies is ok) and playables are human. I have uploaded a townie pool replacement with 8 aliens, in case you want to use them.
Although it's ok if you want to play it all the other way round, I see that could be easier for some people... and you might consider it is humans "visiting" an alien planet, why not?
To be honest, I'm all about CUSTOMIZING the challenge. I don't think I could play any challenge out there without twisting the rules to fit my playstyle so I assume you may need to twist these. Feel free to go ahead!